amorehead

EGNN-DGL

An implementation of the Equivariant Graph Neural Network (EGNN) layer type for DGL-PyTorch.

awesome-equivariant-network

Paper list for equivariant neural network

lightning-hydra-template

PyTorch Lightning + Hydra. A very user-friendly template for rapid and reproducible ML experimentation with best practices. ⚡🔥⚡

amorehead

My GitHub profile header.

FoldFlow

Code release for our recent paper "SE(3)-Stochastic Flow Matching for Protein Backbone Generation" https://arxiv.org/abs/2310.02391

biodiffusion

DiffSBDD

A Euclidean diffusion model for structure-based drug design.

e3nn

A modular framework for neural networks with Euclidean symmetry

geometric-rna-design

Multi-State RNA Design with Geometric Multi-Graph Neural Networks

MLForEveryone

A series of tutorials on learning Machine Learning using the Python programming language, for everyone!

amorehead-portfolYOU

My personal portfolio built using portfolYOU, a beautiful portfolio Jekyll theme that works with GitHub Pages.

atom3

Atomic Data Processing (Python 3 Version)

awesome-expressive-gnn

A collection of papers studying/improving the expressiveness of graph neural networks (GNNs)

biopython

Official git repository for Biopython (originally converted from CVS)

chroma

A generative model for programmable protein design

conditional-flow-matching

TorchCFM: a Conditional Flow Matching library

e3_diffusion_for_molecules

EnQA

A 3D-equivariant neural network for protein structure accuracy estimation

EquiBind

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

FlowSite

foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

geomstats

Computations and statistics on manifolds with geometric structures.

NeMo

NeMo: a toolkit for conversational AI

OmegaFold-Embeddings

OmegaFold Release Code

pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

ProteinWorkshop

ProtMIMO-CodingChallenge

se3_diffusion

Implementation for SE(3) diffusion model with application to protein backbone generation

targetdiff

The official implementation of 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction (ICLR 2023)